Broke Through the Darkness
by katiekayx
Summary: AU after the return from Neverland. For once in Storybrooke, everything is fine, but despite that, Emma decides that the Storybrooke Sheriff's Department could use some help.
1. Part 1

_AU after the return from Neverland. For once in Storybrooke, everything is __**fine**__, and Emma decides that the Storybrooke Sheriff's Department could use some help. _ _I don't own OUAT, the characters, etc etc. Song title is taken from lyrics from the song "Amazing" by Matt Cardle._ _My vision for what Deputy Jones would look like is heavily influenced by Nathan Wuornos from "Haven", because reasons. (exhibit A, exhibit B: hip badge)_

For someone who was convinced that he would never fit in anywhere but on the open sea, Emma is pleased to discover that Captain Hook is fitting in just fine in Storybrooke. It took quite awhile, granted, but after Henry regaled nearly everyone in town with stories about how the once feared pirate Captain rescued him and his entire family from Pan's clutches, the residents of Storybrooke didn't hesitate to welcome him.

It had not been easy at first, she wagered, for him to accept the praise that was being thrust upon him. It made him happy, though, and she found herself constantly hiding smiles whenever she was around him and someone stopped to thank him. That shy smile (one she had only seen on his face once before) would appear and it was in that moment she knew that Killian Jones, not Captain Hook, was here to stay.

After three months, she officially deputizes him, much to her father's (and Neal's) chagrin. Secretly, she thinks David is happy that she won't be going alone on calls anymore. With the reintroduction of magic to Storybrooke, there is no shortage of petty arguments over things that happened years ago in the Enchanted Forest to sort out, and there's always the chance of someone becoming a megalomaniac and trying to take over the town.

Neal is convinced that Killian is going to try to take advantage of his new position, and to Killian's credit, he never tries to defend himself, he just stands quietly by Emma's side (like always), one eyebrow raised incredulously (like always) until she claims that she's heard enough. Neal storms off and Emma tamps down a sigh as she turns around and hands Killian the deputy badge that used to belong to her. He looks at it reverently and she begins to see just how much this symbol of _belonging_ really means to him.

* * *

His first week on the job, he buys himself a new wardrobe. Emma stifles a laugh when he walks in the doors because _really_, and when he starts to take offense, she finds it incredibly endearing. "No, Killian," she starts to explain, (and she tries to ignore the way his eyes soften at the sound of his name coming off her lips) "We match." She says, gesturing to her own outfit.

They both wear jeans (she's 98% sure his are just as tight as hers are), and boots, and their badges clipped to their belts. He wears a fitted navy blue button-up shirt with a leather jacket over top that looks like it was made just for him. She wears a blouse under her own leather jacket, a tan color that her mother had gotten for her in place of her well-worn red one. (The red one, she still keeps, plans on keeping it forever. A part of her acknowledges that it was part of her "armor", and also acknowledges that maybe she doesn't need it so much anymore)

His eyes widen slightly and he lets out a laugh, a carefree sound that she wishes she heard from him more often. "Never let it be said that I don't have impeccable fashion sense, darling," he quips, and positively swaggers over to his newly-constructed desk that sits just outside Emma's office.

"Swan, I…" he trails off, rubbing the back of his neck awkwardly, "I want you to know that I appreciate you doing this for me."

Her brows furrow, "What do you mean?"

He takes a step closer, and she knows before he even speaks that this is one of those moments David always talks about, that it's _important_, and her heart speeds up at the thought.

"This job… this responsibility that you've entrusted me with, it means a lot to me." Emma opens her mouth to speak, but he keeps talking, "Protecting the people of this town, protecting _you_ and your family… this is the type of thing that Liam would have wanted for me. An honorable position." He clears his throat against the sudden onslaught of emotions presenting themselves, "So thank you. Thank you for letting me be Killian Jones again."

Emma doesn't quite know what to say, so she doesn't say anything, just absentmindedly squeezes his hand as she walks past him to the small kitchen. She tries not to feel his gaze burning into her as she walks away.

* * *

The next two months are a blur of break-ins, disturbance calls (usually largely due to Anton, who can't really help it if he makes a lot of noise), and calls about strangers trying to get past the town line. Killian has taken to wearing a gloved prosthetic that doesn't look nearly as menacing as his hook, and Emma almost feels proud when she watches him handle the citizens of the little town. He does it his own way, of course, as is the case when they get a call from Granny that Jefferson and the dwarves are nearly having a showdown in the street outside the diner.

Emma reminds him that Jefferson is not quite stable, and he just rolls his eyes before strolling out the door, his gun clipped to his belt. She follows him and they're soon matching each other stride for stride as the sounds of a heated argument grow louder.

"Alright lads, let's break it up, shall we?" He says, all smooth charm once they find the large group of men taking up nearly the entire street.

"Oh great, it's Captain Innuendo!" Jefferson calls with mock glee, and Emma rolls her eyes and sees a glint appear in Killian's eyes. He always does enjoy a challenge, after all.

"So happy to see you again, Hatter. Care to explain what all the trouble is?"

Jefferson jabs a finger in Leroy's direction, "This one _attacked_ me in the middle of the diner!"

"Leroy…" Emma says warningly, and he puts his hands up as if to say he's completely innocent.

"I didn't attack anyone! He was being rude to Ruby, so I suggested that unless he wanted my picaxe somewhere uncomfortable…"

"You can't go around threatening people, Leroy." Emma grows quickly exasperated, and Killian's hands go to his hips in a show of displeasure that she is _positive _he picked up from her father.

"I think everyone should just go home and settle down, savvy?" Killian says, but the firm tone to his voice shows that this is not just a mere suggestion.

Jefferson sends one last withering glare in Leroy's direction before turning and stalking down the street, his coat flying around his ankles as he goes. The dwarves start to converse among themselves and head back inside the diner.

"Bloody dwarves," Killian mutters, "They're going to start a riot one of these days."

"You settled that one pretty quickly," Emma says with a smirk as they walk back to the station, "I'm starting to think that you don't even need me around to show you the ropes anymore."

He nudges her shoulder, "Ah, but where would I be without my lovely blonde partner?" He asks, winking. Emma rolls her eyes, but can't find it in her to hide her smile. She notices that's happening more and more around him lately.

* * *

As much as she had convinced him she'd be okay on her own, Killian cursed himself for letting her go on this call alone. It was no different than many of the other times they'd been called to the pawn shop over the course of Killian's time as Deputy, except for that Gold had apparently been pushed to the breaking point. Someone had broken into his shop and taken something that had once belonged to Belle, and for whatever reason, he had snapped.

Of course, Killian, Emma and David didn't know this at the time, or else there would have been no chance that they would have let Emma go on her own to take care of it. Killian and David were sprinting down the street now, fresh off of a phone call from a nearby shop keeper who could hear Emma and Gold arguing and was concerned. Killian tried to ignore the rapid beating of his heart at the thought that Emma might be in danger, and instead concentrated on getting to the scene as fast as he could.

The door to the shop was wide open, and Killian could clearly see broken glass and various trinkets scattered all around. He hoped against hope that this was the result of the break-in, and not evidence of a struggle. Passing near one of the open windows, he glanced in and felt his heart stutter to a stop.

Gold had a gun trained on Emma.

He froze in his tracks, causing David to do the same, and he turned to the Prince with wide eyes. "Mate, he's —"

"I know," David said sharply, "We need to try and talk him down."

Killian couldn't process what was happening, couldn't think of anything except that his long-time enemy _had a gun pressed to Emma's head_, and all logical thought seemed to flee when he heard a gunshot.

He ripped himself out of David's grasp and burst into the shop, gun drawn. "Make one more bloody move, Crocodile, and I swear to all the Gods I will end you." He growled, waiting for David to come inside so he could move closer to Emma.

Satisfied that David had a handle on the pawnbroker, Killian crouched down next to Emma, who was clenching her teeth in pain, her hands clenched tight around her leg. "I'm fine," she hissed, and he nearly slapped her hands away so he could examine her wound himself.

"You are not _fine_," he said through grit teeth. "You've been shot." He unwound his black scarf from around his neck and began to wrap it tightly around the bullet wound in Emma's thigh, wincing when a muffled sob worked its way out of her mouth.

"Jesus, that hurts."

"Sorry," he said, "… Gods, Emma, what the bloody hell did you say to him?!"

"I didn't say anything! He's not himself, I don't… I think whoever broke into his shop cursed him or hexed him or something."

His eyes met hers, "Regina?"

The blonde shook her head, "Regina wouldn't have anything to gain by stealing from him."

"Can we talk about this later? We need to get you to the infirmary." His fears were dampened after seeing her and talking to her, but he couldn't stop his hand from shaking as he helped her slowly to her feet.

"Hey." She grasped his good hand tightly, (he tried to ignore the sticky feeling of her blood on him because he was sure it would give him nightmares for weeks to come) "I'm okay." She said firmly, and he nodded, turning to David.

"We need to figure out a way to keep him here. Something's wrong with him."

"I gathered that, thanks," David said, sounding slightly out of breath as he struggled to handcuff Gold to a chair in the shop. "I'll stay here with him and call Regina to see what she can do and if she can help us figure this out. You take Emma to Dr. Whale."

Killian nodded tightly and wrapped an arm around Emma's waist, supporting her weight as they worked their way out of the destroyed shop. On their way out, however, they were nearly run over by Neal, who was sprinting for the store. "Emma? What… I heard a gunshot, and…"

"If you'll kindly step aside, Baelfire, we need to get to the hospital."

Neal's eyes were wide as he took in Emma's limp and the blood on both Emma and Killian's hands. "I can help, let me —"

"Look Neal, I appreciate it, but there's nothing you can do," Emma said, hissing in pain, "I just need to get to the hospital."

"Are you going to be okay?"

"She'll be fine," Killian said firmly, "But if she loses any more blood she'll pass out, and I really don't feel like carrying her all the way there, so if you please," he gestured for Neal to move, and Emma punched his arm. "What the bloody hell was that for?"

"Like carrying me would be _so _hard!"

"Is now really the time for this, Swan?"

"If I'm such a burden, maybe I should just walk there myself!"

Killian's eyes rolled upwards as he heaved a sigh, "For the love of all the gods…" Without another word, he slid his arms under Emma's legs, careful not to jostle her injury and despite her protests, began to carry her in the direction of the hospital.

Neal seemed frozen on the spot, watching them, and Killian narrowed his eyes slightly, "Did you need something? Or would you mind going inside and helping David with your father?"

"I… sure," Neal mumbled, turning and heading inside the shop.

"He doesn't wear jealousy well," Killian remarked.

"Shut up and walk, pirate." Emma said, and he smirked.

"As milady commands."

* * *

When Emma woke up in the hospital, Killian was slouched in the chair next to her bed, eyes trained on her.

"I thought Aurora was the one with the sleeping curse," he commented, his eyes twinkling with mischief.

"How long have I been asleep?"

"Almost an entire day," Killian said, and Emma could see the worry flash in his eyes for a brief moment. "After I brought you in, they operated straight away." He leaned towards her slightly, "You had me worried there for a moment, Swan."

She scoffed, "It was just my leg."

He almost looked angry, and Emma found herself surprised at the emotion playing across his face. "And what if it would have gotten infected, hm? What if they had to amputate your bloody leg?"

"Killian, really."

"I wish you wouldn't be so careless with your life, Emma."

"You're not serious."

He stood, beginning to pace, "Of course I'm serious! From now on, if there's a call from the pawn shop, I'm going to take it, or David."

"Excuse me —"

"I mean it, Emma, if one of us is not with you, I don't want you going in there alone."

"Where do you think you can get off with telling me —"

Killian snapped, turning to face her, "He had a gun to your head!" His voice echoed off the walls, and his eyes were blazing. "How do you think I felt walking in there and seeing you…" he shut his eyes tightly for a moment. "I have never been more terrified because I thought that _monster_ was going to take away someone else that I…" Their eyes locked, and he held her gaze for a beat before dropping it. "That I care about."

A look of understanding washed over Emma's face, and she held out her hand. "Killian… sit down."

He did as she asked, grasping her hand and lacing their fingers together. With a jolt, he realized that they had been holding hands like this for the last few weeks now, whenever the other needed reassurance or comfort. He was always so aware of her, so how did this simple fact seem to escape him?

"I'm fine, okay? He's not himself. He didn't mean to shoot me."

"He —"

"Wait, let me finish. We had no idea what I was walking into when we got that call, or else I wouldn't have gone alone. You know that. I always drag you into life or death situations, don't I?" She smirked at him, drawing a small smile to his lips.

"It is always an adventure with you, that's for certain." He teased, and she squeezed his hand.

"Are you okay, now?"

His sapphire eyes met her green ones, and she was struck by the intensity in them. "I am now that I know you're alright."

"Killian, you know I… I care about you too," she finished, somewhat lamely. She wished that for once she could actually speak her mind.

He smiled at her then, a dazzling smile that rendered her speechless. He furthered her speechlessness by leaning down and placing a soft kiss on her forehead. Pulling back, he whispered, "Please be more careful, Swan. I couldn't bear it if something happened to you."

"I'm sorry. I'll try." Emma knew her honesty wasn't what he wanted to hear, but it was all she could give him.

"Thank you." He knew the combination of fear, concern, and adoration was likely written all over his face, but this time he had no desire to try and hide it. They'd been dancing around each other for too long. He reached out and smoothed her hair away from her forehead.

"Will you stay for awhile?" she sounded oddly vulnerable, and his heart clenched at the sound.

He pulled the chair closer to her bed and grabbed her hand once more. "As you wish, milady."


	2. Part 2

**I got inspired and wrote a second part to this! I am obsessed with modern clothes-wearing, deputy!Killian. I don't know what it is, you guys. Anyway, I hope you like this! Please review and let me know what you think! **

* * *

Emma is waiting for Killian at Granny's, and is trying very hard not to fidget as she glances at her watch and sees that he's running ten minutes late. He's the most punctual person she has ever met, and he is always bragging about being able to tell time without looking at a clock. When she hears the bell above the front door and sees him saunter in, she immediately feels relief sweep through her, although she tries to keep it hidden when he spots her.

He slides into the booth across from her, and grins at her, sending a wink in her direction for good measure. "Swan," he greets, and she frowns before lightly kicking his leg under the table. He jumps, and narrows his eyes at her, "what the hell was that for?"

"You were supposed to be here ten minutes ago! I've been waiting for you," she grumbles, "I could have eaten an hour ago, but since you_ demanded_ I wait for you…"

Killian barely restrains himself from rolling his eyes and tilts his head towards the counter where Ruby is watching them with amusement. "Dear Ruby, would you mind getting the Sheriff here her meal before she becomes even more cross with me?"

"You got it, Captain," Ruby says, complete with a salute, and Emma swears Killian's head is going to explode with the rate that his ego is growing. Since rescuing Henry from Neverland and becoming her deputy, Killian had quickly grown to be the town hero, and his roguish charms have worked their wiles on everyone, even Ruby and Granny.

"Now, what were you yelling at me for?" He asks, arching an eyebrow at her before perusing a menu (useless, she thought, because he got the same thing every time he came here).

"It's not very good form," she stretches the words out, mocking him, "to leave someone waiting."

"Emma, honestly. It was ten minutes." He looks at her, eyes narrowed before crossing his arms over his chest (a chest that had on a new, burgundy hoodie, not that she was noticing things like that…). "You want to tell me what's really bothering you? And don't lie to me, lass, we both know that won't get us anywhere."

Emma looks down at her lap. "I don't know what you're talking about."

"Swan," He starts, shaking his head in frustration, but is interrupted by Ruby bringing Emma's cheeseburger, and Killian's usual – a grilled cheese with a hot bowl of tomato soup. He told her once that it reminded him of something his mother used to make for him and Liam when they were younger, and she couldn't ever remember seeing a more wistful look on his face than when he was reliving that memory.

Emma takes that moment to change the subject, not wanting to dwell on the fact that he had been late, and he was never late, and how, for a horrifying second, she had been convinced that something had happened to him. "I have a doctor's appointment tomorrow morning, so you and David are going to have to go on patrol together."

He grimaces, although she knows that he and David are quickly becoming best friends, and that he doesn't mind spending time with her father. "I suppose I'll find a way to go on without you, Swan." He says dramatically, clutching at his chest. His eyes twinkle with amusement, and she struggles to stay irritated with him. His eyes turn serious when she rubs at her knee absentmindedly. "How's your leg?" He asks, referring to their latest adventure – after a disturbance call from Mr. Gold's Pawn Shop had led to Gold being affected by something, a curse most likely, he had shot Emma in the leg. Killian had been furious, and had carried Emma the entire way to the hospital, where she had undergone surgery immediately. The bullet hadn't done that much damage, but it had shaken the both of them up, and Killian's insistence that Emma not go on any calls alone to Gold's shop anymore had left a strange tension in their partnership.

"It doesn't bother me much, but Dr. Whale just wants to check and make sure everything is healing the way it's supposed to," Emma says, shrugging.

"Do you want me to go with you?" He asks, the gentleman in him coming out, and something inside Emma's heart clenches at the sincerity in his words.

"You don't have to, Killian." She says softly, and she wonders how it is that they reached this point. She knew the minute that they got back from Neverland that things were going to change, but she never anticipated this. She hasn't had a partner in her entire life, sans Graham, and she (understandably) had anxiety about making Killian her deputy after what had happened to the Huntsman.

As for the "fun" that Killian had promised would happen between the two of them… well. Nothing had really changed. Their trust in one another had increased to the point it was unwavering, and he remained at her side, like he had through their entire journey to Neverland, but now it was second nature. He didn't do it because it was expected, or because he was trying to prove himself to her. He did it because he was her partner, and her friend.

Emma wasn't naïve, though. She knew there was something there between the two of them. They were affectionate at times, like in the hospital after she had been shot. Killian had sat with her the entire night, and held her hand as he told her that he couldn't bear it if something happened to her. That night had changed things between them, as they both laid their vulnerabilities on the table for the other to see. Emma had stopped trying to deny that she was attracted to the pirate-turned-deputy, and knew that she cared for him more than she was ready to admit, but she didn't know how to initiate what she wanted with him. She wasn't even sure that he still cared for her as much as he had during their time in Neverland. He still flirted with everything that moved, although part of her was sure that his flirting and his cocky swagger was a defense mechanism that he had perfected over the years to prevent himself from getting hurt.

His lilting accent brought her out of her thoughts. "That's not what's bothering you, is it." It wasn't a question.

Emma squirms in her seat, hating how he could read her so well. She knows it shouldn't be bothering her, but she can't stop feeling the anxiety that had consumed her when he had been running late, her mind obsessing over the many horrible scenarios that could have befallen him in Storybrooke. It bothered her more than she wanted to acknowledge that the simple thought of something happening to him was enough to nearly give her a breakdown. "I just… next time you're going to be late, at least call me okay?"

Killian's eyes soften, and he reaches across the table to grip her hand briefly. "I'm sorry, Emma. I didn't mean to worry you, I just lost track of time."

He goes back to eating, although he keeps his eyes on her and she suddenly doesn't feel hungry anymore. "You know what? I'm tired. I think I'm going to go home and go to bed early."

She grabs her coat and leaves a bill on the table for her meal and is out the door before he can protest, although she hears him calling after her as she hurries down the street, trying to get a reign on her emotions before he can catch up to her.

* * *

Killian only allows himself to stare dumbfounded after her for a moment before he practically runs out of the diner after her. "Emma!"

She stops, but she doesn't turn around, and he can't stop the sinking feeling in his stomach that something is wrong, that _he_ did something wrong, and he hates thinking that he's disappointed her or made her upset. Things have been so good between them lately that he feels almost like he had taken it for granted.

He jogs up to her, standing in front of her in the middle of the street. He touches her arm gently, trying to remain calm, but starting to feel angry when he notices how she won't meet his eyes. "Swan." His voice is firm, and she tenses at his tone, pulling away from him. He takes a deep breath. "Have I done something to upset you?"

She finally looks at him, and the turmoil in her eyes nearly breaks him. "_Emma,_" he breathes, begging her to tell him what's wrong.

"It's just…" she huffs in frustration, rolling her eyes at her unusual show of emotion. "You were late, and you're never late, and I thought maybe something had happened to you!" She blurts, and his eyes widen.

She had been worried about him. Worried about _him_. "Emma -"

"And I know you said you just lost track of the time, and maybe you were with someone or whatever, and that's _fine_, but I didn't know that, and after everything that's happened over the last few weeks, I was… I was concerned, and I just…"

"Wait, wait." He says, holding up a hand, his voice taking on an incredulous tone, "you thought I was _with someone_?" He asks, using air quotes.

"Well how was I supposed to know what you were doing?!"

"Seven hells, Emma," he runs a hand through his hair, "How in all the realms could you _possibly_ think…" he trails off, letting out a frustrated breath, "how could you even think for a minute that I would spend any time with anyone else after everything you and I have been through?" His voice is raw, honest, and hoarse, and he almost doesn't recognize the emotions lacing his words, although he knows what they are, of course he does.

She's frozen, staring back at him like she can't believe what he's saying, and he doesn't know how else to make her see, how to make her understand that she is _everything_ except to kiss her. So he does.

He moves forward and in one smooth move, he slides a hand behind her neck and pulls her closer, his mouth slanting over hers in a kiss that makes her gasp, and causes a shudder to run all the way to his toes. It's reminiscent of their kiss in Neverland, one that seems like it took place eons ago, but this one is more desperate as he struggles to tell her in words what she means to him. She makes a small noise in the back of her throat and it makes something inside of him snap, and he hauls her to him bodily, causing a groan to rip itself out of his chest as their bodies press together.

His mind is a blur, all his thoughts coated with a haze of pleasure as lust courses throughout his body as she kisses him back, and her hands are in his hair, tugging at it, causing his hips to roll into hers once, and twice, and he breaks away with a broken groan, needing air.

It's silent, both of them staring at each other with fire in their eyes, and Killian takes a step backwards, knowing that they are treading into dangerous territory. "The way I feel about you… that has never changed, Emma. I just don't know what you want from me."

"Killian…"

"Don't misunderstand me, Emma. I am so grateful for what you've given me." He gestures vaguely to the town around them, "You've given me a chance to have a home again, and a real, proper profession," he grins then, a small, shy thing, "and of course, the chance to spend my days with the lovely Sheriff." He winks at her, and feels validated when a pretty blush spreads over her cheeks. "But, Emma… you run so hot and cold with me. One minute we're holding hands and you're worried about me when I'm only a few minutes late, and the next, you're shutting me and practically running down the street to get away from me."

Emma is quiet for a long moment before she takes a deep breath and begins speaking, her voice so quiet that he has to take a step closer to hear her. "You know that I don't… I don't deal with my emotions well. So when I realized that maybe my concern for you as my partner was bordering on concern for you as… as someone that I cared about, well, I just… I freaked out." She reaches for him, and he doesn't hesitate in lacing their fingers together. "Somehow, you've managed to knock down all those walls I've built up to protect myself." He can see tears starting to well in her eyes, and he knows that she wouldn't be showing this side of her to anyone else. His heart swells at the thought, and grips her hand tighter. "I care about you, Killian. Probably more than I should, probably more than I ever intended to let myself."

"Emma, you _know_ that I care about you. You know that I…" He swallows thickly, debating for a second on his next words, but they seem to spill out of him. "I'm in love with you, you stubborn woman." He whispers the last bit, feeling as if a weight lifts off of him as he lets go of the words that have been on the tip of his tongue whenever he was around her for the last few months.

Emma takes a step towards him and places her hands gently on the side of his face, leaning her forehead against his. She takes a shaky breath, and he knows that she is struggling with what to say to him, but he doesn't care. He doesn't care, because she is touching him and she's not running away.

"You don't have to say anything," he whispers, his eyes fluttering closed when her hands move to his hair.

"You're blushing, Captain." She says, and his eyes snap open at the husky quality to her voice and when he sees her teasing smile, he can't restrain himself anymore. He kisses her again, long and slow, and a quiet whimper from Emma nearly makes him forget that they are in the middle of town where anyone could see them.

"Minx," he growls when they pull apart, and she laughs, the breathless sound one that he wants to hear again and again. "I should walk you home," he says, and she shakes her head.

"I don't want to go home."

His eyes widen at the certainty in her voice. "Swan?"

"You're always bragging about what a comfortable bed you've got on that ship of yours, aren't you?" She teases, and then lets out a very un-Emma-like squeal when he hoists her up into his arms.

"Are you sure about this, Princess?"

"I can handle it if you can, pirate." She retorts, and he grins.

"I never was one to back down from a challenge, Sheriff."

She silences him with another kiss, and he relishes in the feeling of familiarity that washes over him at the feel of her pressed against him. Whatever happens tomorrow, he knows that they're starting another adventure, one that he hopes will last for the rest of his life.

* * *

**Thanks for reading, and if you liked it, let me know! Also make sure you're following me on Tumblr, ( .com) where I frequently take fic prompts for CS and other pairings! :)**


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